Abstract
The microbiome is essential for host health, and perturbations resulting from antibiotic use can lead to dysbiosis and disease. Diet can be a powerful modulator of microbiome composition and function, with the potential to mitigate the negative effects of antibiotic use. Thus, it is necessary to study the impacts of diet and drug interactions on the gut microbiome. Coffee is a commonly consumed beverage containing many compounds that have the potential to affect the microbiome, including caffeine, polyphenols, and fiber. We supplemented mice with caffeinated and decaffeinated coffee in conjunction with amoxicillin, and used 16S rRNA amplicon sequencing of fecal samples to investigate changes in diversity and composition of the murine fecal microbiome. We found that antibiotics, regardless of coffee supplementation, caused significant disruption to the murine fecal microbiome, enriching for Proteobacteria, Verrucomicrobia, and Bacteroidetes, but reducing Firmicutes. While we found that coffee alone did not have a significant impact on the composition of the fecal microbiome, coffee supplementation did significantly affect relative abundance metrics in mice treated with amoxicillin. After caffeinated coffee supplementation, mice treated with amoxicillin showed a smaller increase in Proteobacteria, specifically of the family Burkholderiaceae. Correspondingly we found that in vitro, Burkholderia cepacia was highly resistant to amoxicillin, and that it was inhibited by concentrations of caffeine and caffeinated coffee comparable to levels of caffeine in murine ceca. Overall, this work shows that coffee, and possibly the caffeine component, can impact both the microbiome and microbiome members during antibiotic exposure.
Highlights
The human gut is home to trillions of bacteria which are vital for many host processes, including energy extraction from food, synthesis of important molecules, and protection from pathogens (Becattini et al, 2016)
Because Proteobacteria are strongly associated with dysbiotic microbiomes (Becattini et al, 2016), we further investigated the impact of coffee and caffeine on Burkholderiaceae in vitro. 16S analysis does not allow us to accurately characterize bacteria down to the species level, so we chose to utilize B. cepacia as a model from the Burkholderiaceae family to investigate the impact of coffee and amoxicillin
We found that neither caffeinated nor decaffeinated coffee alone has a major impact on the diversity or composition of the murine fecal microbiome
Summary
The human gut is home to trillions of bacteria which are vital for many host processes, including energy extraction from food, synthesis of important molecules, and protection from pathogens (Becattini et al, 2016) These microorganisms and their genetic content are collectively referred to as the gut microbiome. The oxygen content of the gut increases, leading to decreased fermentation by obligate anaerobes and diminished SCFA production. This in turn decreases gut barrier integrity, which leads to inflammation and promotes the growth of facultative aerobic bacteria such as Proteobacteria (Jha et al, 2019). Some members of this phylum are opportunistic pathogens and are highly immunogenic, such as Escherichia coli and Klebsiella spp., and have the potential for expansion under dysbiotic conditions (Becattini et al, 2016; Kim et al, 2017; Zarrinpar et al, 2018)
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